BN1614 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.6883e-05 1.3924e-03
Layer 5 5.8766e-05 1.1292e-03
Layer 6 1.3497e-04 1.6900e-03
Layer 3 3.3594e-04 3.6956e-02
Layer 2 2.1343e-03 9.2328e-02
WM 6.1341e-02 1.8394e-01
Layer 1 9.3426e-01 7.7651e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
TUBB2A Expression Distribution
Gene Specificity Score (GSS)
TUBB2A GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
TUBB2A Layer 5 2.8594 0.7517
SH3GL2 Layer 6 2.4785 0.7509
SYN2 Layer 5 2.7480 0.7479
ENO2 Layer 5 2.7070 0.7478
TBR1 Layer 5 2.5215 0.7436
CHGA Layer 4 2.8975 0.7366
SYP Layer 5 2.7480 0.7358
DYNLRB1 Layer 4 2.5029 0.7340
SNRPN Layer 5 2.5391 0.7333
RAB6B Layer 5 2.5781 0.7300
NDRG4 Layer 5 2.5664 0.7260
SNCA Layer 5 2.8057 0.7256
SYN1 Layer 6 2.5723 0.7250
FXYD6 Layer 5 2.7422 0.7243
ATP5F1B Layer 4 2.5176 0.7238
MLLT11 Layer 5 2.6719 0.7236
UBE2QL1 Layer 5 2.2969 0.7233
EEF1A2 Layer 5 2.7480 0.7224
SSBP3 Layer 5 2.6836 0.7221
SERPINI1 Layer 5 2.6367 0.7215
MYO5A Layer 5 2.8516 0.7199
BMERB1 Layer 5 2.5176 0.7194
STMN2 Layer 5 2.8457 0.7164
PFKP Layer 4 2.5566 0.7161
ANK2 Layer 5 2.6367 0.7158
TAGLN3 Layer 4 2.8252 0.7156
CYFIP2 Layer 5 2.3965 0.7148
SCAMP5 Layer 6 2.3281 0.7148
YWHAH Layer 5 2.5059 0.7146
SLC9A6 Layer 5 2.4512 0.7138
PRKAR1B Layer 5 2.7852 0.7134
FAIM2 Layer 5 2.4844 0.7129
UQCRH Layer 5 2.4336 0.7123
SNAP91 Layer 5 2.6895 0.7120
NAPB Layer 5 2.6309 0.7111
USP11 Layer 6 2.3711 0.7110
REEP5 Layer 5 2.3340 0.7110
GOT1 Layer 5 2.4180 0.7110
DNAJC6 Layer 5 2.5117 0.7104
NDUFS5 Layer 5 2.3555 0.7100
RAB3A Layer 6 2.4785 0.7089
PKM Layer 4 2.4395 0.7083
TUBB Layer 5 2.4316 0.7080
TMEM130 Layer 5 2.5215 0.7079
APBB1 Layer 4 2.3086 0.7077
ATP1A1 Layer 5 2.4512 0.7066
PNMA2 Layer 5 2.6191 0.7061
PREPL Layer 5 2.4639 0.7059
DNM1 Layer 6 2.5215 0.7056
YPEL3 Layer 4 2.4482 0.7051

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1614
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1614_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1614/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1614/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1614/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1614/report/PD/BN1614_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1614/report/PD/BN1614_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:33:32
  • Number of Processes: 10
  • Spending Time: 0h 3m